Physics of Life Reviews最新文献

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The second law of thermodynamics, life and Earth‘s planetary machinery revisited 热力学第二定律、生命与地球行星机械的再认识

IF 13.7 1区生物学 Q1 BIOLOGY

Physics of Life Reviews

Pub Date : 2024-10-22 DOI: 10.1016/j.plrev.2024.10.009

Axel Kleidon

Life is a planetary feature that depends on its environment, but it has also strongly shaped the physical conditions on Earth, having created conditions highly suitable for a productive biosphere. Clearly, the second law of thermodynamics must apply to these dynamics as well, but how? What insights can we gain by placing life and its effects on planetary functioning in the context of the second law? In Kleidon (2010), I described a thermodynamic Earth system perspective by placing the functioning of the Earth system in terms of the second law. The Earth system is represented by a planetary hierarchy of energy transformations that are driven predominantly by incoming solar radiation, these transformations are constrained by the second law, but they are also modified by the feedbacks from various dissipative activities. It was then hypothesised that life evolves its dissipative activity to the limits imposed by this hierarchy and evolves feedbacks aimed at pushing these limits to higher levels of dissipative activity. Here I provide an update of this perspective. I first review applications to climate and global climate change to demonstrate its success in predicting magnitudes of physical processes, particularly regarding temperatures, heat redistribution and hydrological cycling. I then focus on the limits to dissipative activity of the biosphere. It would seem that the limitations by thermodynamics act indirectly by imposing limitations associated with transport and material exchange. I substantiate this interpretation and discuss the broader implications for habitability, the emergence and evolution of life, and the contemporary biosphere.

生命是一种依赖于环境的行星特征，但它也在很大程度上塑造了地球的物理条件，创造了非常适合生产生物圈的条件。显然，热力学第二定律也必须适用于这些动力学，但如何适用呢？将生命及其对地球运作的影响置于第二定律的背景下，我们能获得哪些启示？在 Kleidon（2010 年）一书中，我从热力学的角度描述了地球系统，将地球系统的运作置于第二定律的背景下。地球系统由主要由太阳辐射驱动的能量转换的行星层次结构来表示，这些转换受到第二定律的制约，但也受到各种耗散活动的反馈作用的影响。当时的假设是，生命在耗散活动的演化过程中会受到这种层次结构的限制，并会产生旨在将这些限制推向更高水平的耗散活动的反馈。在此，我将对这一观点进行更新。我首先回顾了该方法在气候和全球气候变化方面的应用，以证明其在预测物理过程的大小，特别是温度、热量再分配和水文循环方面的成功。然后，我将重点讨论生物圈耗散活动的限制。热力学的限制似乎是通过施加与运输和物质交换相关的限制来间接发挥作用的。我将证实这一解释，并讨论其对宜居性、生命的出现和进化以及当代生物圈的广泛影响。

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引用次数: 0

A brigde toward mathematics theory in living systems: the thermostatted kinetic theory method for crowd dynamics 迈向生命系统数学理论的第一步：人群动力学的恒温动力学理论方法：对 Carlo Bianca 的评论文章 "复杂活性物质生命系统的恒温动力学理论模型十年 "的评论。

IF 13.7 1区生物学 Q1 BIOLOGY

Physics of Life Reviews

Pub Date : 2024-10-21 DOI: 10.1016/j.plrev.2024.10.007

Christian Dogbe

引用次数: 0

Disentangled representations for causal cognition 因果认知的分离表征

IF 13.7 1区生物学 Q1 BIOLOGY

Physics of Life Reviews

Pub Date : 2024-10-21 DOI: 10.1016/j.plrev.2024.10.003

Filippo Torresan , Manuel Baltieri

Complex adaptive agents consistently achieve their goals by solving problems that seem to require an understanding of causal information, information pertaining to the causal relationships that exist among elements of combined agent-environment systems. Causal cognition studies and describes the main characteristics of causal learning and reasoning in human and non-human animals, offering a conceptual framework to discuss cognitive performances based on the level of apparent causal understanding of a task. Despite the use of formal intervention-based models of causality, including causal Bayesian networks, psychological and behavioural research on causal cognition does not yet offer a computational account that operationalises how agents acquire a causal understanding of the world seemingly from scratch, i.e. without a-priori knowledge of relevant features of the environment. Research on causality in machine and reinforcement learning, especially involving disentanglement as a candidate process to build causal representations, represents on the other hand a concrete attempt at designing artificial agents that can learn about causality, shedding light on the inner workings of natural causal cognition. In this work, we connect these two areas of research to build a unifying framework for causal cognition that will offer a computational perspective on studies of animal cognition, and provide insights in the development of new algorithms for causal reinforcement learning in AI.

复杂的适应性代理一直通过解决似乎需要了解因果信息的问题来实现其目标，这些信息涉及代理-环境组合系统中各元素之间存在的因果关系。因果认知研究并描述了人类和非人类动物因果学习和推理的主要特征，提供了一个概念框架，根据对任务的明显因果理解程度来讨论认知表现。尽管使用了正式的基于干预的因果关系模型，包括因果关系贝叶斯网络，但关于因果认知的心理学和行为学研究还没有提供一个可操作的计算账户，说明行为主体如何在似乎从零开始的情况下，即在没有环境相关特征的先验知识的情况下，获得对世界的因果理解。另一方面，对机器学习和强化学习中因果关系的研究，特别是将解缠作为建立因果表征的候选过程的研究，则是设计能够学习因果关系的人工代理的具体尝试，为自然因果认知的内部运作提供了启示。在这项工作中，我们将这两个研究领域联系起来，建立了一个统一的因果认知框架，为动物认知研究提供了一个计算视角，并为人工智能中因果强化学习新算法的开发提供了启示。

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引用次数: 0

The sound of thought: Form matters–The prosody of inner speech 思想的声音：形式很重要--内心言语的韵律。

IF 13.7 1区生物学 Q1 BIOLOGY

Physics of Life Reviews

Pub Date : 2024-10-18 DOI: 10.1016/j.plrev.2024.10.006

Hamutal Kreiner , Zohar Eviatar

This paper offers a new perspective on inner speech based on the theoretical framework of embodiment, focusing on the embodiment of structure rather than content. We argue that inner speech is used to simulate the acoustic aspects of overt speech including prosody. Prosody refers to the rhythm, intonation, and stress of spoken language, which is closely related to structural aspects of phrases, sentences, and larger language contexts such as discourse and narrative. We propose that inner speech gives form and structure to thought, and that this form is a necessary component of mental life. Thus, our paper opens with a review of the varieties of inner speech, followed by evidence concerning the form of inner speech, and finally, we discuss the functionality of inner speech. We consider cognitive and socio-emotional functions in which inner speech is involved and posit that inner speech serves as a simulation that maintains form and that this form serves different aspects of thought – attention, memory, emotion and self- regulation, social conceptualization, and narrative of self. In concluding, we address future research asking how inner speech contributes to making mental processes accessible to conscious thought, and whether accessibility to consciousness is related to form and structure.

本文基于 "体现"（embodiment）的理论框架，对内心言语提出了一个新的视角，重点关注结构而非内容的体现。我们认为，内心言语用于模拟公开言语的声学方面，包括前奏。前奏是指口语的节奏、语调和重音，与短语、句子以及话语和叙事等更大的语言环境的结构密切相关。我们认为，内在言语赋予思维以形式和结构，这种形式是精神生活的必要组成部分。因此，我们的论文首先回顾了内心言语的种类，然后提出了有关内心言语形式的证据，最后讨论了内心言语的功能。我们考虑了内在言语所涉及的认知和社会情感功能，并认为内在言语是一种保持形式的模拟，这种形式服务于思维的不同方面--注意力、记忆、情感和自我调节、社会概念化和自我叙述。最后，我们将探讨未来的研究，即内在言语如何帮助意识思维获得心理过程，以及意识思维的获得是否与形式和结构有关。

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引用次数: 0

More than one effect in every affect 每种影响都有一种以上的效果

IF 13.7 1区生物学 Q1 BIOLOGY

Physics of Life Reviews

Pub Date : 2024-10-18 DOI: 10.1016/j.plrev.2024.10.008

Antonino Costanzo , Alessandro Musetti , Rodolfo Rossi , Adriano Schimmenti

引用次数: 0

Determinism of formamide-based biogenic prebiotic reactions 甲酰胺类生物源生物反应的决定性。

IF 13.7 1区生物学 Q1 BIOLOGY

Physics of Life Reviews

Pub Date : 2024-10-16 DOI: 10.1016/j.plrev.2024.10.004

Raffaele Saladino, Bruno Mattia Bizzarri, Ernesto Di Mauro

Formamide reacted in the presence of a catalyst and of a source of energy affords a rich and complex panel of compounds, including amino acids, amino sugars, nucleic bases, nucleosides, carboxylic acids, aliphatic chains, and more. Nor the source of energy nor the type of catalyst are fastidious. All the catalysts tested have activity; each catalyst affords its own specific set of products, although the panels of products of each catalyst largely overlap. Potentially biogenic compounds form in reasonable conditions and the chemistry that determines the initial syntheses is facile. Hence, Darwins warm little pond did not rely on exotic environments nor on magic tricks. The type of molecules resulting from a mixture of formamide and of two selected products of its initial reactions hint that the initial prebiotic soup was deterministic and oriented towards life-as-we-know-it.

甲酰胺在催化剂和能量源的存在下发生反应，可产生丰富而复杂的化合物，包括氨基酸、氨基糖、核酸、核苷、羧酸、脂肪链等。对能量来源和催化剂类型的要求都不严格。所有测试过的催化剂都具有活性；每种催化剂都能提供自己特定的一组产物，尽管每种催化剂的产物板在很大程度上是重叠的。潜在的生物化合物在合理的条件下形成，决定初始合成的化学反应也很简单。因此，达尔文温暖的小池塘并不依赖于奇异的环境或魔术。甲酰胺和其初始反应的两种精选产物的混合物所产生的分子类型暗示，最初的前生物汤是确定性的，是面向我们所知的生命的。

引用次数: 0

Update on “Emotion and autobiographical memory”: 14 years of advances in understanding functions, constructions, and consequences 情感与自传体记忆 "的最新进展：14 年来在了解功能、构造和后果方面取得的进展

IF 13.7 1区生物学 Q1 BIOLOGY

Physics of Life Reviews

Pub Date : 2024-10-16 DOI: 10.1016/j.plrev.2024.10.005

Leonard Faul, Jaclyn H. Ford, Elizabeth A. Kensinger

Holland and Kensinger (2010) reviewed the literature on “Emotion and autobiographical memory.” They focused on two broad ways that emotions influence memory: (1) emotion during an event influences how the event is remembered, and (2) emotion and emotional goals during memory retrieval influence how past events are remembered. We begin by providing a brief update on the key points from that review. Holland and Kensinger (2010) also had noted a number of important avenues for future work. Here, we describe what has been learned about the functions of autobiographical memory and their reconstructive nature. Relatedly, we review more recent research on memory reconstruction in the context of visual perspective shifts, counterfactual thinking, nostalgia, and morality. This research has emphasized the reciprocal nature of the interactions between emotion and autobiographical memory: Not only do emotions influence memory, memories influence emotions. Next, we discuss advances that have been made in understanding the reciprocal relations between stress, mood, and autobiographical memory. Finally, we discuss the research that is situating emotional autobiographical memories within a social framework, providing a bedrock for collective memories. Despite the many advances of the past 14 years, many open questions remain; throughout the review we note domains in which we hope to see advances over the next decades.

Holland 和 Kensinger（2010 年）回顾了有关 "情绪与自传体记忆 "的文献。他们重点讨论了情绪影响记忆的两大途径：(1) 事件发生时的情绪会影响事件的记忆方式；(2) 记忆检索时的情绪和情绪目标会影响过去事件的记忆方式。我们首先简要介绍一下该综述的最新要点。Holland 和 Kensinger（2010 年）还指出了未来工作的一些重要途径。在此，我们将介绍有关自传体记忆的功能及其重构性质的研究成果。与此相关，我们回顾了最近在视觉视角转换、反事实思维、怀旧和道德背景下对记忆重建的研究。这些研究强调了情绪与自传体记忆之间相互作用的相互性：不仅情绪影响记忆，记忆也影响情绪。接下来，我们将讨论在理解压力、情绪和自传体记忆之间的相互关系方面所取得的进展。最后，我们将讨论将情绪自传体记忆置于社会框架内的研究，为集体记忆提供基石。尽管在过去的 14 年中取得了许多进展，但仍有许多悬而未决的问题；在整个综述中，我们指出了我们希望在未来几十年中看到进展的领域。

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引用次数: 0

A technical comment on “A decade of thermostatted kinetic theory models for complex active matter living systems”. New fascinating perspectives of research 关于 "复杂活性物质生命系统恒温动力学理论模型的十年 "的技术评论。引人入胜的研究新视角

IF 13.7 1区生物学 Q1 BIOLOGY

Physics of Life Reviews

Pub Date : 2024-10-11 DOI: 10.1016/j.plrev.2024.10.002

Massimiliano Ferrara

引用次数: 0

The emotional grounds of existence: A phenomenologist's view. Commentary to “The affective grounds of the mind. The affective pertinentization (APER) model” by Salvatore et al. 存在的情感基础：现象学家的观点。对萨尔瓦多等人所著 "心灵的情感基础：情感相关化（APER）模型 "的评论。情感相关化（APER）模型 "的评论。

IF 13.7 1区生物学 Q1 BIOLOGY

Physics of Life Reviews

Pub Date : 2024-10-10 DOI: 10.1016/j.plrev.2024.10.001

Giovanni Stanghellini

引用次数: 0

Ant colony optimization: A bibliometric review 蚁群优化：文献综述

IF 13.7 1区生物学 Q1 BIOLOGY

Physics of Life Reviews

Pub Date : 2024-09-26 DOI: 10.1016/j.plrev.2024.09.014

Christian Blum

This paper is a follow-up of one of the most-cited articles published in the first 20 years of the existence of Physics of Life Reviews. The specific topic is “ant colony optimization”, which is a metaheuristic for solving challenging optimization problems. Due to its inspiration from natural ant colonies' shortest path-finding behavior, this optimization technique forms part of a larger field known as swarm intelligence. After a short introduction to ant colony optimization, we first provide a chronology focusing on algorithmic developments rather than applications. The main part of the paper deals with a bibliometric study of the ant colony optimization literature. Interesting trends concerning, for example, the geographic origin of publications and the change in research focus over time, can be learned from the presented graphs and numbers.

本文是《生命物理学评论》创刊 20 年来发表的被引用次数最多的文章之一的后续文章。具体主题是 "蚁群优化"，这是一种用于解决具有挑战性的优化问题的元启发式方法。由于其灵感来自于自然界蚁群的最短路径搜索行为，这种优化技术构成了一个更大领域的一部分，即 "蚁群智能"。在简要介绍了蚁群优化之后，我们首先提供了一份年表，重点介绍算法的发展而非应用。论文的主要部分是蚁群优化文献的文献计量学研究。从图表和数字中可以了解到一些有趣的趋势，例如出版物的地域来源和研究重点的变化。

引用次数: 0

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